Conservation and relative importance of residues across protein-protein interfaces
M Guharoy, P Chakrabarti - Proceedings of the National …, 2005 - National Acad Sciences
A core region surrounded by a rim characterizes biological interfaces. We ascertain the
importance of the core by showing the sequence entropies of the residues comprising the …
importance of the core by showing the sequence entropies of the residues comprising the …
Protein-protein interfaces: architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences
CJ Tsai, SL Lin, HJ Wolfson… - Critical reviews in …, 1996 - Taylor & Francis
Protein structures generally consist of favorable folding motifs formed by specific
arrangements of secondary structure elements. Similar architectures can be adopted by …
arrangements of secondary structure elements. Similar architectures can be adopted by …
Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations
The significant work that has been invested toward understanding protein− protein
interaction has not translated into significant advances in structure-based predictions. In …
interaction has not translated into significant advances in structure-based predictions. In …
An analysis of conformational changes on protein–protein association: implications for predictive docking
MJ Betts, MJE Sternberg - Protein Engineering, 1999 - academic.oup.com
Conformational changes on complex formation have been measured for 39 pairs of
structures of complexed proteins and unbound equivalents, averaged over interface and …
structures of complexed proteins and unbound equivalents, averaged over interface and …
Rapid refinement of protein interfaces incorporating solvation: application to the docking problem
RM Jackson, HA Gabb, MJE Sternberg - Journal of molecular biology, 1998 - Elsevier
A computationally tractable strategy has been developed to refine protein-protein interfaces
that models the effects of side-chain conformational change, solvation and limited rigid-body …
that models the effects of side-chain conformational change, solvation and limited rigid-body …
Protein–protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states …
Energetic hot spots account for a significant portion of the total binding free energy and
correlate with structurally conserved interface residues. Here, we map experimentally …
correlate with structurally conserved interface residues. Here, we map experimentally …
ProFace: a server for the analysis of the physicochemical features of protein-protein interfaces
Background Molecular recognition is all pervasive in biology. Protein molecules are
involved in enzyme regulation, immune response, signal transduction, oligomer assembly …
involved in enzyme regulation, immune response, signal transduction, oligomer assembly …
[PDF][PDF] Morphology of protein–protein interfaces
TA Larsen, AJ Olson, DS Goodsell - Structure, 1998 - cell.com
Background: Most soluble proteins are active as low-number oligomers. Statistical surveys
of oligomeric proteins have defined the roles of hydrophobicity and complementarity in the …
of oligomeric proteins have defined the roles of hydrophobicity and complementarity in the …
EvoDesign: designing protein–protein binding interactions using evolutionary interface profiles in conjunction with an optimized physical energy function
Abstract EvoDesign (https://zhanglab. ccmb. med. umich. edu/EvoDesign) is an online
server system for protein design. The method uses evolutionary profiles to guide the …
server system for protein design. The method uses evolutionary profiles to guide the …
Protein–protein docking: is the glass half-full or half-empty?
S Vajda, CJ Camacho - TRENDS in Biotechnology, 2004 - cell.com
Are current docking methods capable of building complexes from putative component
protein structures? Results of recent computational studies, including those of the CAPRI …
protein structures? Results of recent computational studies, including those of the CAPRI …